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Yorodumi- PDB-4uyp: High resolution structure of the third cohesin ScaC in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uyp | ||||||
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Title | High resolution structure of the third cohesin ScaC in complex with the ScaB dockerin with a mutation in the N-terminal helix (IN to SI) from Acetivibrio cellulolyticus displaying a type I interaction. | ||||||
Components | (Cellulosomal scaffoldin ...) x 2 | ||||||
Keywords | CELL ADHESION/PROTEIN BINDING / CELL ADHESION-PROTEIN BINDING COMPLEX / CELLULOSOME / TYPE 1 COHESIN-DOCKERIN INTEREACTIONS / ADAPTOR SCAFFOLDIN SCAB / ANCHORING SCAFFOLDING SCAC | ||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Acetivibrio cellulolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Cameron, K. / Alves, V.D. / Bule, P. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2015 Title: Cell-surface Attachment of Bacterial Multienzyme Complexes Involves Highly Dynamic Protein-Protein Anchors. Authors: Cameron, K. / Najmudin, S. / Alves, V.D. / Bayer, E.A. / Smith, S.P. / Bule, P. / Waller, H. / Ferreira, L.M. / Gilbert, H.J. / Fontes, C.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Purification, Crystallization and Preliminary X-Ray Characterization of the Acetivibrio Cellulolyticus Type I Cohesin Scac in Complex with the Scab Dockerin. Authors: Cameron, K. / Alves, V.D. / Bule, P. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uyp.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uyp.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/4uyp ftp://data.pdbj.org/pub/pdb/validation_reports/uy/4uyp | HTTPS FTP |
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-Related structure data
Related structure data | 4uyqC 2cclS 4uzp C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Cellulosomal scaffoldin ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 16512.172 Da / Num. of mol.: 2 / Fragment: RESIDUES 326-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q7WYN2 #2: Protein | Mass: 8382.468 Da / Num. of mol.: 2 / Fragment: RESIDUES 868-942 / Mutation: I822S, N833I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q7WYN3 |
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-Non-polymers , 5 types, 666 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-MPD / ( #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): FROM THE CRYSTALLISATION CONDITION. (4S)- ...4-(2-HYDROXYETH |
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Sequence details | THE THIRD COHESIN CORRESPONDS TO RESIDUES 326 TO 427 OF THE ANCHORING SCAFFOLDIN SCAC. IT HAS A HIS ...THE THIRD COHESIN CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.5 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 30%(V/V) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→76.19 Å / Num. obs: 96788 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.49→1.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCL Resolution: 1.49→76.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.002 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.162 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→76.19 Å
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Refine LS restraints |
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